Sequence Comparison of Five Polymerases (L proteins) of Unsegmented Negative-strand RNA Viruses: Theoretical Assignment of Functional Domains

Abstract

The large (L) protein subunit of unsegmented negativestrand RNA virus polymerases is thought to be responsible for the majority of enzymic activities involved in viral transcription and replication. In order to gain insight into this multifunctional role we compared the deduced amino acid sequences of five L proteins of rhabdoviruses (vesicular stomatitis virus and rabies virus) or paramyxoviruses (Sendai virus, Newcastle disease virus and measles virus). Statistical analysis showed that they share an atypical amino acid usage, outlining the uniqueness of the negative-strand virus life style. Similarity studies between L proteins traced evolutionary relationships in partial disagreement with the present taxonomic arrangement of this group of viruses. The five L proteins exhibit a high degree of homology along most of their length, with strongly invariant amino acids embedded in conserved blocks separated by variable regions, suggesting a structure of concatenated functional domains. The most highly conserved central block contains the probable active site for RNA synthesis. We tentatively identified some other functional sites, distributed around this central core, that would naturally work together to assure the polymerase activity. This provides detailed guidelines for the future study of L proteins by site-directed mutagenesis.

Complete sequence of the genome of avian paramyxovirus type 2 (strain Yucaipa) and comparison with other paramyxoviruses

“…Amino acid alignment of domain III of the L proteins of selected members of family Paramyxoviridae. The putative polymerase core motifs (A, B, C and D) are boxed within domain III (Poch et al, 1990). Amino acid identity with APMV-2 (top line) is indicated by dots, while gaps introduced to maximize amino acid identity are indicated by dashes.…”

“…The extent of amino acid sequence identity with the L proteins of members of the other general of Paramyxovirinae decreased in the order: rubulaviruses (37.5%), respiroviruses (31.2%), morbilliviruses (30.3 %), and henipaviruses (25.2-25.7 %). The six stronglyconserved linear domains of L proteins of nonsegmented negative-strand RNA viruses (Poch et al, 1990) are also identified within the L protein of strain Yucaipa (Fig. 5).…”

Genomic sequence of mandarin fish rhabdovirus with an unusual small non-transcriptional ORF

“…The putative L protein consists of 2078 aa with a calculated molecular mass of 237.5 kDa and a pI of 8.03. Multiple sequence alignment revealed the six conserved blocks (blocks I-VI) which have previously been reported in comparisons of mononegavirales L proteins (Poch et al, 1990) and are located between aa 223 and 1701 of SCRV L protein. Blocks II and III are the most conserved blocks among the six blocks, and contain five conserved motifs, pre-A-D (Poch et al, 1989;Muller et al, 1994) (Fig.…”

“…Six conserved blocks were identified by multiple alignments of the L proteins of rhabdoviruses as described previously (Poch et al, 1990). Blocks II and III are most conserved among the six blocks.…”

Characterisation of a proposed Nucleorhabdovirus new to South Africa

“…The blocks of conservation were designated blocks I-VI, of which blocks II-V, located in the central region of the L protein, have relative high amino acid conservation. Block III of the polymerase protein has the highest amino acid conservation and is conserved among all RNA-dependent RNA polymerases (Poch et al 1990;Bourhy et al 2005).…”